Biopolym. Cell. 2010; 26(1):36-44.
Structure and Function of Biopolymers
Hydration change on complexation of aromatic ligands with DNA: molecular dynamics simulations
1Kostjukov V. V., 1Khomutova N. M., 1Evstigneev M. P.
  1. Sevastopol National Technical University
    33, Universytetska Str., Sevastopol, Ukraine, 99053


Aim. Analysis of the hydration changes at formation of DNA complexes with biologically active aromatic compounds (BAC): antibiotics actinomycin D, daunomycin, nogalamycin, novantrone and mutagens ethidium bromide and proflavine. Methods. Molecular dynamics simulations. Results. The hydration indexes for double-helical DNA and ligands in a free and complexed states were calculated. A critical analysis of modern ideas about changing water environment at binding of aromatic ligands to DNA was performed. Conclusions. It is shown that upon binding of aromatic BAC with DNA a significant (from 2.6 for novantrone to 13.1 for actinomycin D) liberation of water molecules out of hydration shells with the disruption of hydrogen bonds takes place.
Keywords: double-helical DNA, aromatic ligand, hydration index, water release


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